Stoke forward Xherdan Shaqiri's winner nine minutes from time consigned Newcastle to a sixth straight away loss in the Premier League and kept them mired in the relegation zone.
The Magpies, back in action after 18 days off, arrived at the Britannia Stadium having not picked up a point on the road since a December 13 win at Tottenham, while they also had been eliminated from the FA Cup with a loss at Watford in January.
A point would have lifted them out of the bottom three, and they were on course to ensure a share of the spoils at the Britannia Stadium before Shaqiri popped up with a moment of magic in the Potters' 1-0 win.
The Swiss international collected substitute Mame Diouf's lay off and smashed a left-footed attempt beyond Rob Elliot in the Magpies goal.
It was enough to earn Mark Hughes' side a third win on the spin, yet they needed a fantastic one-handed save from Jack Butland to repel Seydou Doumbia in stoppage time as Newcastle almost grabbed an unlikely leveller.
Shaqiri's goal was almost upstaged by Arnautovic with the last kick of the game, the Austrian's fine volley clattering against the crossbar just before the final whistle sounded.